Removed debug prints, only zero atom forces and not copy them, added measurements

src/force.cu

@@ -111,26 +111,14 @@ double computeForce(
         )
 {
     int Nlocal = atom->Nlocal;
-    MD_FLOAT* fx = atom->fx;
-    MD_FLOAT* fy = atom->fy;
-    MD_FLOAT* fz = atom->fz;
 #ifndef EXPLICIT_TYPES
     MD_FLOAT cutforcesq = param->cutforce * param->cutforce;
     MD_FLOAT sigma6 = param->sigma6;
     MD_FLOAT epsilon = param->epsilon;
 #endif
-    printf("-1\r\n");
 
     cudaProfilerStart();
 
-    printf("0\r\n");
-
-    for(int i = 0; i < Nlocal; i++) {
-        fx[i] = 0.0;
-        fy[i] = 0.0;
-        fz[i] = 0.0;
-    }
-
     const char *num_threads_env = getenv("NUM_THREADS");
     int num_threads = 0;
     if(num_threads_env == nullptr)
@@ -145,8 +133,6 @@ double computeForce(
     c_atom.Nmax = atom->Nmax;
     c_atom.ntypes = atom->ntypes;
 
-    printf("0.1\r\n");
-
     /*
     int nDevices;
     cudaGetDeviceCount(&nDevices);
@@ -167,8 +153,6 @@ double computeForce(
     // HINT: Run with cuda-memcheck ./MDBench-NVCC in case of error
     // HINT: Only works for data layout = AOS!!!
 
-    printf("1\r\n");
-
     if(!initialized) {
         checkCUDAError( "c_atom.x malloc", cudaMalloc((void**)&(c_atom.x), sizeof(MD_FLOAT) * atom->Nmax * 3) );
         checkCUDAError( "c_atom.fx malloc", cudaMalloc((void**)&(c_atom.fx), sizeof(MD_FLOAT) * Nlocal) );
@@ -183,13 +167,11 @@ double computeForce(
         checkCUDAError( "c_neigh_numneigh malloc", cudaMalloc((void**)&c_neigh_numneigh, sizeof(int) * Nlocal) );
     }
 
-    printf("2\r\n");
+    checkCUDAError( "c_atom.fx memset", cudaMemset(c_atom.fx, 0, sizeof(MD_FLOAT) * Nlocal) );
+    checkCUDAError( "c_atom.fy memset", cudaMemset(c_atom.fy, 0, sizeof(MD_FLOAT) * Nlocal) );
+    checkCUDAError( "c_atom.fz memset", cudaMemset(c_atom.fz, 0, sizeof(MD_FLOAT) * Nlocal) );
 
-    if(reneighbourHappenend || !initialized) {
     checkCUDAError( "c_atom.x memcpy", cudaMemcpy(c_atom.x, atom->x, sizeof(MD_FLOAT) * atom->Nmax * 3, cudaMemcpyHostToDevice) );
-        checkCUDAError( "c_atom.fx memcpy", cudaMemcpy(c_atom.fx, fx, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyHostToDevice) );
-        checkCUDAError( "c_atom.fy memcpy", cudaMemcpy(c_atom.fy, fy, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyHostToDevice) );
-        checkCUDAError( "c_atom.fz memcpy", cudaMemcpy(c_atom.fz, fz, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyHostToDevice) );
     checkCUDAError( "c_atom.type memcpy", cudaMemcpy(c_atom.type, atom->type, sizeof(int) * atom->Nmax, cudaMemcpyHostToDevice) );
     checkCUDAError( "c_atom.epsilon memcpy", cudaMemcpy(c_atom.epsilon, atom->epsilon, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
     checkCUDAError( "c_atom.sigma6 memcpy", cudaMemcpy(c_atom.sigma6, atom->sigma6, sizeof(MD_FLOAT) * atom->ntypes * atom->ntypes, cudaMemcpyHostToDevice) );
@@ -197,13 +179,6 @@ double computeForce(
 
     checkCUDAError( "c_neigh_numneigh memcpy", cudaMemcpy(c_neigh_numneigh, neighbor->numneigh, sizeof(int) * Nlocal, cudaMemcpyHostToDevice) );
     checkCUDAError( "c_neighs memcpy", cudaMemcpy(c_neighs, neighbor->neighbors, sizeof(int) * Nlocal * neighbor->maxneighs, cudaMemcpyHostToDevice) );
-    }
-
-    printf("3\r\n");
-
-    printf("4\r\n");
-
-    printf("5\r\n");
 
     const int num_threads_per_block = num_threads; // this should be multiple of 32 as operations are performed at the level of warps
     const int num_blocks = ceil((float)Nlocal / (float)num_threads_per_block);
@@ -216,16 +191,11 @@ double computeForce(
     checkCUDAError( "PeekAtLastError", cudaPeekAtLastError() );
     checkCUDAError( "DeviceSync", cudaDeviceSynchronize() );
 
-    printf("6\r\n");
-
     // copy results in c_atom.fx/fy/fz to atom->fx/fy/fz
-    if(reneighbourHappenend) {
+
     cudaMemcpy(atom->fx, c_atom.fx, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyDeviceToHost);
     cudaMemcpy(atom->fy, c_atom.fy, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyDeviceToHost);
     cudaMemcpy(atom->fz, c_atom.fz, sizeof(MD_FLOAT) * Nlocal, cudaMemcpyDeviceToHost);
-    }
-
-    printf("7\r\n");
 
     /*
     cudaFree(c_atom.x);

src/main.c

@@ -111,20 +111,13 @@ double reneighbour(
 {
     double S, E;
 
-    printf("10.1\r\n");
-
     S = getTimeStamp();
     LIKWID_MARKER_START("reneighbour");
-    printf("10.2\r\n");
     updateAtomsPbc(atom, param);
-    printf("10.3\r\n");
     setupPbc(atom, param);
-    printf("10.4\r\n");
     updatePbc(atom, param);
-    printf("10.5\r\n");
     //sortAtom(atom);
     buildNeighbor(atom, neighbor);
-    printf("10.6\r\n");
     LIKWID_MARKER_STOP("reneighbour");
     E = getTimeStamp();
 
@@ -288,18 +281,12 @@ int main(int argc, char** argv)
         const bool doReneighbour = (n + 1) % param.every == 0;
         const bool doesReneighbourNextRound = (n + 2) % param.every == 0;
 
-        printf("Run %d does reneighbour: %d\r\n", n, doReneighbour);
-
-        printf("10\r\n");
-
         if(doReneighbour) {
             timer[NEIGH] += reneighbour(&param, &atom, &neighbor);
         } else {
             updatePbc(&atom, &param);
         }
 
-        printf("11\r\n");
-
         if(param.force_field == FF_EAM) {
             timer[FORCE] += computeForceEam(&eam, &param, &atom, &neighbor, &stats, 0, n + 1);
         } else {

src/neighbor.c

@@ -172,8 +172,6 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor)
 {
     int nall = atom->Nlocal + atom->Nghost;
 
-    printf("nall: %d, nmax: %d\r\n", nall, nmax);
-
     /* extend atom arrays if necessary */
     if(nall > nmax) {
         nmax = nall;
@@ -185,14 +183,10 @@ void buildNeighbor(Atom *atom, Neighbor *neighbor)
         // neighbor->neighbors = (int*) malloc(nmax * neighbor->maxneighs * sizeof(int*));
     }
 
-    printf("10.5.1\r\n");
-
     /* bin local & ghost atoms */
     binatoms(atom);
     int resize = 1;
 
-    printf("10.5.2\r\n");
-
     /* loop over each atom, storing neighbors */
     while(resize) {
         int new_maxneighs = neighbor->maxneighs;
@@ -322,14 +316,9 @@ int coord2bin(MD_FLOAT xin, MD_FLOAT yin, MD_FLOAT zin)
 
 void binatoms(Atom *atom)
 {
-    printf("10.5.1.1\r\n");
     int nall = atom->Nlocal + atom->Nghost;
     int resize = 1;
 
-    printf("10.5.1.2\r\n");
-
-    printf("nall: %d, atom->Nmax: %d\r\n", nall, atom->Nmax);
-
     while(resize > 0) {
         resize = 0;
 
@@ -337,8 +326,6 @@ void binatoms(Atom *atom)
             bincount[i] = 0;
         }
 
-        printf("10.5.1.3\r\n");
-
         for(int i = 0; i < nall; i++) {
             MD_FLOAT x = atom_x(i);
             MD_FLOAT y = atom_y(i);
@@ -353,15 +340,11 @@ void binatoms(Atom *atom)
             }
         }
 
-        printf("10.5.1.4\r\n");
-
         if(resize) {
             free(bins);
             atoms_per_bin *= 2;
             bins = (int*) malloc(mbins * atoms_per_bin * sizeof(int));
         }
-
-        printf("10.5.1.5\r\n");
     }
 }